跳到正文
cccskills
免费在 GitHub 公开

cp2k-geo-opt

CP2K geometry optimization. Handles bulk, slab, and molecular systems with GPW method. Efficient for large systems (200+ atoms).

中文简介正在准备中。当前显示原文说明。

Hello-QM/catgo-LRG星标 208(GitHub 208 + cccskills 0)

实测评分 未实测

查看安装方法

包含的文件(1)

  • SKILL.md7.0 KB

SKILL.md(原文)

安装前可以查看交给 AI 代理的指令内容。

CP2K Geometry Optimization

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.

Scenario 1: Bulk Optimization

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"})

Scenario 2: Slab Optimization

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 bulk
  • poisson_solver="MT" — Martyna-Tuckerman solver handles the vacuum correctly for 2D-periodic systems. Use "PERIODIC" for bulk (3D-periodic) and "MT" or "WAVELET" for slabs

Scenario 3: Adsorbate on Slab

Same 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")

Scenario 4: Large System (500+ atoms)

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:

  • OT: O(N) scaling, no HOMO-LUMO gap requirement, default for > 100 atoms
  • Diagonalization: O(N^3) scaling, needed for metallic systems (zero gap)

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")

Key Parameters

ParameterDefaultPurpose
cutoff600 RyPW cutoff for density grid
rel_cutoff60 RyMulti-grid relative cutoff
basis_setDZVP-MOLOPT-SR-GTHGaussian basis set
xc_functionalPBEExchange-correlation functional
max_iter200Max geometry optimization steps
eps_geo3e-4Force convergence (Hartree/Bohr, ~ 0.015 eV/A)
eps_scf1e-6SCF convergence (Hartree)
cell_optFalseWhether to optimize cell parameters
freeze_layers0Number of bottom layers to freeze
vdw_methodNoneDispersion correction ("DFTD3", "DFTD3(BJ)")
poisson_solverPERIODICPoisson solver ("PERIODIC", "MT", "WAVELET")

Convergence Monitoring

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"})

Chain: CP2K Optimization then Frequency

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()

Output

The geo_opt task produces:

  • output.structure — optimized structure (pymatgen dict as JSON string)
  • output.energy — total DFT energy in eV

Troubleshooting

ProblemFix
SCF not convergingUse OT method, increase scf_max_iter, reduce mixing
Energy oscillationsIncrease cutoff (try 800 Ry), check rel_cutoff
Forces not convergingLoosen eps_geo, increase max_iter
OT fails for metalSwitch to diagonalization with Fermi smearing
Memory errorReduce cutoff, use SZV basis, increase nodes
Missing basis for elementCheck CP2K basis set library, may need to download
Poisson solver error for slabUse poisson_solver="MT" instead of "PERIODIC"

Unit Conversions

CP2K uses atomic units internally. CatGo converts automatically, but for reference:

  • 1 Hartree = 27.2114 eV
  • 1 Bohr = 0.529177 A
  • Force: 1 Ha/Bohr = 51.422 eV/A
  • eps_geo=3e-4 Ha/Bohr corresponds to ~0.015 eV/A (comparable to VASP EDIFFG=-0.02)

评价

还没有评价。欢迎分享你的使用感受。

评论

无需登录即可发表。欢迎分享使用感受、提问,或说明在哪些环境下无法运行。

还没有评论。来写第一条吧。

提交后会立即公开。请勿填写邮箱、电话等个人信息。URL 最多 2 个。

0 / 1000 字

此表单受 reCAPTCHA 保护,适用 Google 的隐私权政策和服务条款。

同一仓库的技能

abinit

免费

Generate and manage ABINIT DFT calculations. Use when the user requests ABINIT, or needs DFPT phonons, GW calculations, or BSE optical spectra.

中文简介正在准备中。当前显示原文说明。

Hello-QM/catgo-LRG2082026年10月23日 更新

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.

中文简介正在准备中。当前显示原文说明。

Hello-QM/catgo-LRG2082026年10月23日 更新

Use when the user asks for adsorption energy, binding energy, or wants to compare how strongly a molecule binds to a surface.

中文简介正在准备中。当前显示原文说明。

Hello-QM/catgo-LRG2082026年10月23日 更新

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.

中文简介正在准备中。当前显示原文说明。

Hello-QM/catgo-LRG2082026年10月23日 更新

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.

中文简介正在准备中。当前显示原文说明。

Hello-QM/catgo-LRG2082026年10月23日 更新

atom-ops

免费

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 ....

中文简介正在准备中。当前显示原文说明。

Hello-QM/catgo-LRG2082026年10月23日 更新

查看 Hello-QM 的全部技能

报告此技能的问题