abinit
無料Generate and manage ABINIT DFT calculations. Use when the user requests ABINIT, or needs DFPT phonons, GW calculations, or BSE optical spectra.
日本語の概要は準備中です。原文の説明を表示しています。
CP2K geometry optimization. Handles bulk, slab, and molecular systems with GPW method. Efficient for large systems (200+ atoms).
日本語の概要は準備中です。原文の説明を表示しています。
実行スコア 未検証
インストール方法を見るインストールする前に、エージェントに与えられる指示の中身を確認できます。
Set up and submit CP2K geometry optimizations using the Gaussian and Plane-Wave (GPW) method. CP2K is the preferred code for systems larger than ~200 atoms where VASP becomes memory-limited.
Full cell and ionic relaxation for periodic bulk systems.
from catgo.workflow import Workflow
wf = Workflow("CP2K bulk MgO")
struct = wf.add_task("structure_input", structure=bulk_json)
opt = wf.add_task("geo_opt",
structure=struct.output.structure,
software="cp2k",
cell_opt=True, # Relax cell + ions (like ISIF=3 in VASP)
cutoff=600, # Ry
rel_cutoff=60, # Ry
basis_set="DZVP-MOLOPT-SR-GTH",
xc_functional="PBE",
max_iter=200, # Max geo_opt steps
eps_geo=3e-4, # Force convergence (Hartree/Bohr)
system_name="bulk_MgO")
wf.submit()
MCP equivalent:
catgo_workflow_v2(action="create", params={"name": "CP2K bulk MgO"})
catgo_workflow_v2(action="add_task", params={
"workflow_id": "wf_xxx",
"task_type": "structure_input",
"structure": "<bulk_json>"
})
catgo_workflow_v2(action="add_task", params={
"workflow_id": "wf_xxx",
"task_type": "geo_opt",
"software": "cp2k",
"structure": "{{t_001.output.structure}}",
"cell_opt": true,
"cutoff": 600,
"basis_set": "DZVP-MOLOPT-SR-GTH",
"system_name": "bulk_MgO"
})
catgo_workflow_v2(action="submit", params={"workflow_id": "wf_xxx"})
Fixed cell, ionic relaxation with frozen bottom layers. Analogous to VASP ISIF=2.
wf = Workflow("CP2K TiO2 slab")
struct = wf.add_task("structure_input", structure=slab_json)
opt = wf.add_task("geo_opt",
structure=struct.output.structure,
software="cp2k",
cell_opt=False, # Fix cell (slab)
cutoff=600,
basis_set="DZVP-MOLOPT-SR-GTH",
freeze_layers=2, # Freeze bottom 2 layers
poisson_solver="MT", # Martyna-Tuckerman for slab geometry
system_name="TiO2_slab")
wf.submit()
Slab-specific settings:
cell_opt=False — mandatory for slabs (equivalent to ISIF=2 in VASP)freeze_layers=2 — freeze bottom layers to mimic bulkpoisson_solver="MT" — Martyna-Tuckerman solver handles the vacuum correctly for 2D-periodic systems. Use "PERIODIC" for bulk (3D-periodic) and "MT" or "WAVELET" for slabsSame as slab, with adsorbate atoms free to relax:
opt = wf.add_task("geo_opt",
structure=adsorbate_slab_json,
software="cp2k",
cell_opt=False,
freeze_layers=2,
cutoff=600,
vdw_method="DFTD3", # Dispersion for adsorption
poisson_solver="MT",
system_name="*OH_on_TiO2")
CP2K's GPW method with OT (Orbital Transformation) SCF solver scales linearly for large systems:
opt = wf.add_task("geo_opt",
structure=large_system_json,
software="cp2k",
cutoff=400, # Lower cutoff acceptable for screening
basis_set="SZV-MOLOPT-SR-GTH", # Minimal basis for speed
ot_minimizer="DIIS", # OT method for large systems
ot_preconditioner="FULL_ALL",
eps_scf=1e-5,
system_name="large_system")
OT vs diagonalization:
For metals: OT does not work for metallic systems (zero band gap). Use Fermi-Dirac smearing with diagonalization:
opt = wf.add_task("geo_opt",
structure=metal_json,
software="cp2k",
scf_method="diag", # Standard diagonalization
smearing_method="FERMI_DIRAC",
electronic_temperature=300, # K
system_name="metal")
| Parameter | Default | Purpose |
|---|---|---|
| cutoff | 600 Ry | PW cutoff for density grid |
| rel_cutoff | 60 Ry | Multi-grid relative cutoff |
| basis_set | DZVP-MOLOPT-SR-GTH | Gaussian basis set |
| xc_functional | PBE | Exchange-correlation functional |
| max_iter | 200 | Max geometry optimization steps |
| eps_geo | 3e-4 | Force convergence (Hartree/Bohr, ~ 0.015 eV/A) |
| eps_scf | 1e-6 | SCF convergence (Hartree) |
| cell_opt | False | Whether to optimize cell parameters |
| freeze_layers | 0 | Number of bottom layers to freeze |
| vdw_method | None | Dispersion correction ("DFTD3", "DFTD3(BJ)") |
| poisson_solver | PERIODIC | Poisson solver ("PERIODIC", "MT", "WAVELET") |
catgo_workflow_v2(action="status", params={"workflow_id": "wf_xxx"})
catgo_analyze(action="convergence", params={"task_id": "t_opt"})
# Returns: energy vs step, max force vs step
catgo_analyze(action="forces", params={"task_id": "t_opt"})
wf = Workflow("CP2K opt + freq")
struct = wf.add_task("structure_input", structure=slab_oh_json)
opt = wf.add_task("geo_opt", structure=struct.output.structure,
software="cp2k", freeze_layers=2,
system_name="*OH")
frq = wf.add_task("freq", structure=opt.output.structure,
software="cp2k",
freeze_mode="layers", freeze_layers=4,
system_name="*OH")
gib = wf.add_task("gibbs_energy",
energy=opt.output.energy,
frequencies=frq.output.frequencies,
phase="adsorbed", system_name="*OH")
wf.submit()
The geo_opt task produces:
output.structure — optimized structure (pymatgen dict as JSON string)output.energy — total DFT energy in eV| Problem | Fix |
|---|---|
| SCF not converging | Use OT method, increase scf_max_iter, reduce mixing |
| Energy oscillations | Increase cutoff (try 800 Ry), check rel_cutoff |
| Forces not converging | Loosen eps_geo, increase max_iter |
| OT fails for metal | Switch to diagonalization with Fermi smearing |
| Memory error | Reduce cutoff, use SZV basis, increase nodes |
| Missing basis for element | Check CP2K basis set library, may need to download |
| Poisson solver error for slab | Use poisson_solver="MT" instead of "PERIODIC" |
CP2K uses atomic units internally. CatGo converts automatically, but for reference:
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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.
日本語の概要は準備中です。原文の説明を表示しています。
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.
日本語の概要は準備中です。原文の説明を表示しています。
Use when the user asks for adsorption energy, binding energy, or wants to compare how strongly a molecule binds to a surface.
日本語の概要は準備中です。原文の説明を表示しています。
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.
日本語の概要は準備中です。原文の説明を表示しています。
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.
日本語の概要は準備中です。原文の説明を表示しています。
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 ....
日本語の概要は準備中です。原文の説明を表示しています。