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cccskills
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catgo-workflow

Create and manage computational chemistry workflows with CatGo. Supports VASP, CP2K, ORCA, MLP, LAMMPS. Build OER/HER/CO2RR workflows, geometry optimization, frequency analysis, Gibbs energy calculations.

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。

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

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インストール方法を見る

含まれるファイル（140）

  • SKILL.md3.8 KB
  • __init__.py1.1 KB
  • builtins_impl.py21.2 KB
  • builtins.py4.7 KB
  • config.py6.5 KB
  • db.py25.3 KB
  • engine/__init__.py615 B
  • engine/advancer.py9.3 KB
  • engine/ai_diagnosis.py3.8 KB
  • engine/batch_submitter.py9.7 KB
  • engine/broadcast.py1.8 KB
  • engine/collector.py8.3 KB
  • engine/control_flow.py5.7 KB
  • engine/engine_builtins.py19.6 KB
  • engine/engine_registry.py1.5 KB
  • engine/error_handler.py3.6 KB
  • engine/hpc_utils.py4.0 KB
  • engine/job_script.py11.6 KB
  • engine/lifecycle.py10.8 KB
  • engine/orca_progress.py3.4 KB
  • engine/poller.py11.7 KB
  • engine/resolver.py2.7 KB
  • engine/result_collector.py56.3 KB
  • engine/result_handler.py5.6 KB
  • engine/scanner.py52.0 KB
  • engine/smart_recovery.py3.6 KB
  • engine/submitter.py26.2 KB
  • engine/v1_monitor.py2.7 KB
  • engine/vasp_submission.py29.0 KB
  • graph_converter.py6.5 KB
  • mcp_tools.py7.5 KB
  • provenance.py5.8 KB
  • reference.py1.1 KB
  • service.py4.0 KB
  • skills/abinit/SKILL.md3.8 KB
  • skills/analysis/adsorption/SKILL.md5.5 KB
  • skills/analysis/charge/SKILL.md5.5 KB
  • skills/analysis/co2rr/SKILL.md8.8 KB
  • skills/analysis/cohp/SKILL.md5.3 KB
  • skills/analysis/convergence/SKILL.md5.6 KB
  • skills/analysis/dos_analysis/SKILL.md5.6 KB
  • skills/analysis/energy_diagram/SKILL.md7.1 KB
  • skills/analysis/gibbs/SKILL.md5.8 KB
  • skills/analysis/her/SKILL.md6.8 KB
  • skills/analysis/mace_ni_benchmark/README.md5.1 KB
  • skills/analysis/mace_ni_benchmark/SKILL.md5.0 KB
  • skills/analysis/nrr/SKILL.md7.7 KB
  • skills/analysis/oer/SKILL.md7.1 KB
  • skills/analysis/phonopy/SKILL.md5.5 KB
  • skills/analysis/reacnetgen/SKILL.md4.5 KB
  • skills/analysis/SKILL.md3.4 KB
  • skills/analysis/volcano/SKILL.md5.3 KB
  • skills/backend_doctor/SKILL.md7.5 KB
  • skills/campaign/references/catgo-cli.md1.8 KB
  • skills/campaign/scripts/aggregate.py1011 B
  • skills/campaign/scripts/archive.py1.8 KB
  • skills/campaign/scripts/campaign_analysis.py4.3 KB
  • skills/campaign/scripts/campaign_lib.py24.5 KB
  • skills/campaign/scripts/campaign_lit.py3.3 KB
  • skills/campaign/scripts/campaign_report.py1.6 KB
  • skills/campaign/scripts/fetch_ref.py943 B
  • skills/campaign/scripts/INDEX.md1.8 KB
  • skills/campaign/scripts/ingest_lit.py1.3 KB
  • skills/campaign/scripts/make_report.py880 B
  • skills/campaign/scripts/new_campaign.py932 B
  • skills/campaign/scripts/poll.py798 B
  • skills/campaign/scripts/submit_calc.py1.6 KB
  • skills/campaign/scripts/test_campaign_analysis.py3.7 KB
  • skills/campaign/scripts/test_campaign_lib.py21.8 KB
  • skills/campaign/scripts/test_campaign_lit.py2.0 KB
  • skills/campaign/scripts/test_campaign_report.py1.4 KB
  • skills/campaign/scripts/test_entrypoints.py2.7 KB
  • skills/campaign/scripts/test_skill_structure.py1.8 KB
  • skills/campaign/scripts/test_vasp_sanity.py9.6 KB
  • skills/campaign/scripts/vasp_sanity.py12.5 KB
  • skills/campaign/SKILL.md6.2 KB
  • skills/campaign/templates/saa_her/plan.md1009 B
  • skills/catgo-campaign-conventions/SKILL.md2.7 KB
  • skills/catgo-campaign-loop/SKILL.md3.9 KB
  • skills/catgo-campaign/SKILL.md4.1 KB
  • skills/catgo-gibbs-pipeline/examples/orr-pt111.md1.8 KB
  • skills/catgo-gibbs-pipeline/references/method.md5.4 KB
  • skills/catgo-gibbs-pipeline/scripts/build_freq_inputs.py4.7 KB
  • skills/catgo-gibbs-pipeline/SKILL.md2.7 KB
  • skills/data/dpdata/SKILL.md4.2 KB
  • skills/data/openbabel/SKILL.md3.9 KB
  • skills/data/packmol/SKILL.md4.3 KB
  • skills/data/SKILL.md1.0 KB
  • skills/deepmd/inference/SKILL.md3.7 KB
  • skills/deepmd/SKILL.md1.5 KB
  • skills/deepmd/train/SKILL.md4.6 KB
  • skills/dftbplus/SKILL.md4.3 KB
  • skills/gaussian/SKILL.md4.7 KB
  • skills/gpaw/SKILL.md4.0 KB
  • skills/lammps/deepmd/SKILL.md4.0 KB
  • skills/lammps/reaxff/SKILL.md4.8 KB
  • skills/lammps/SKILL.md1.8 KB
  • skills/molecular/antechamber/SKILL.md4.5 KB
  • skills/molecular/rdkit/SKILL.md4.5 KB
  • skills/molecular/SKILL.md970 B
  • skills/orca/freq/SKILL.md4.7 KB
  • skills/orca/neb_ts/SKILL.md5.1 KB
  • skills/orca/opt/SKILL.md4.4 KB
  • skills/orca/SKILL.md4.1 KB
  • skills/qe/SKILL.md3.8 KB
  • skills/siesta/SKILL.md3.9 KB
  • skills/SKILL.md8.5 KB
  • skills/structure/adsorbate/SKILL.md11.9 KB
  • skills/structure/atom_ops/SKILL.md4.8 KB
  • skills/structure/cluster_ops/SKILL.md7.7 KB
  • skills/structure/defect/SKILL.md4.8 KB
  • skills/structure/doping/SKILL.md6.2 KB
  • skills/structure/fetch/SKILL.md4.8 KB
  • skills/structure/heterostructure/SKILL.md6.7 KB
  • skills/structure/intercalation/SKILL.md5.3 KB
  • skills/structure/moire/SKILL.md4.4 KB
  • skills/structure/nanotube/SKILL.md4.2 KB
  • skills/structure/SKILL.md4.4 KB
  • skills/structure/slab/SKILL.md7.8 KB
  • skills/structure/strain/SKILL.md5.0 KB
  • skills/structure/substitution/SKILL.md5.3 KB
  • skills/troubleshooting/cluster_config_test/SKILL.md4.1 KB
  • skills/troubleshooting/convergence_issues/SKILL.md5.3 KB
  • skills/troubleshooting/SKILL.md3.7 KB
  • skills/troubleshooting/vasp_errors/SKILL.md4.9 KB
  • skills/troubleshooting/workflow_errors/SKILL.md5.8 KB
  • skills/vasp/band/SKILL.md6.5 KB
  • skills/vasp/dos/SKILL.md5.6 KB
  • skills/vasp/freq/SKILL.md7.5 KB
  • skills/vasp/md/SKILL.md6.3 KB
  • skills/vasp/relax/SKILL.md7.4 KB
  • skills/vasp/SKILL.md4.7 KB
  • skills/vasp/static/SKILL.md5.9 KB
  • skills/workflow_builder/SKILL.md12.3 KB
  • state_map.py1.5 KB
  • states.py7.5 KB
  • task_decorator.py2.5 KB
  • task_ids.py986 B
  • v1_compat.py2.8 KB
  • workflow.py12.0 KB

SKILL.md（原文）

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。

CatGo Workflow Skill

Quick Start — Python API

from catgo.workflow import Workflow
from catgo.workflow.builtins import geo_opt, freq, gibbs_energy

wf = Workflow("RuO2 OER")

# Input structure
slab = wf.add_task("structure_input", structure=structure_json)

# Geometry optimization → Frequency → Gibbs Energy
opt = wf.add_task(geo_opt, structure=slab.output.structure, ENCUT=520, system_name="*OH")
frq = wf.add_task(freq, structure=opt.output.structure, system_name="*OH",
                   freeze_mode="layers", freeze_layers=4)
gib = wf.add_task(gibbs_energy, energy=opt.output.energy,
                   frequencies=frq.output.frequencies, system_name="*OH")

wf.submit()  # Engine picks it up automatically

HPC Confirmation Gate: By default, HPC tasks pause at PENDING_REVIEW after local preprocessing completes, so users can verify structures and parameters before spending HPC resources. Users confirm via the frontend "Confirm & Submit" button (per-task or "Confirm All"). To skip this gate, call wf.submit(auto_submit=True).

HPC Confirmation Required: Before calling wf.submit() or catgo_workflow_engine(action="submit"), you MUST ask the user which HPC cluster to use and confirm job parameters (partition, account, walltime, ntasks). These can be set per-task via add_task params. Never submit without user confirmation.

Available Task Types

HPC Calculations

  • geo_opt — Geometry optimization (VASP/CP2K/ORCA/MLP)
  • single_point — Single point energy (VASP/CP2K/ORCA)
  • freq — Vibrational frequencies (VASP/CP2K/ORCA)
  • cell_opt — Cell optimization (VASP/CP2K)
  • md — Molecular dynamics (VASP/CP2K/LAMMPS/MLP)
  • ts_search — Transition state search (Sella/ORCA NEB-TS)

Local Analysis

  • gibbs_energy — G = E_DFT + ZPE - TS
  • free_energy_diagram — Plot reaction energy diagram
  • dos_analysis — Density of states analysis
  • charge_analysis — Bader charge analysis

Structure Building

  • structure_input — Provide input structure
  • slab_gen — Generate surface slab
  • adsorbate_place — Place adsorbate on surface

Key Parameters

VASP

  • software="vasp", ENCUT, EDIFF, EDIFFG, NSW, ISIF, IBRION
  • ISMEAR, SIGMA, ISPIN, NCORE, KPAR

Frequency

  • freeze_mode: "none", "layers", "z_range", "element", "indices", "manual"
  • freeze_layers: number of bottom layers to freeze
  • freeze_z_below: freeze atoms below this z coordinate (Angstrom)

Gibbs Energy

  • phase: "adsorbed" (harmonic) or "gas" (ideal gas)
  • temperature: K (default 298.15)
  • freq_cutoff: cm-1 (default 50, for adsorbed phase)

Output References

Connect tasks by passing .output.key:

opt.output.structure   # optimized structure
opt.output.energy      # DFT energy (eV)
frq.output.frequencies # vibrational frequencies
frq.output.zpe         # zero-point energy
gib.output.gibbs       # Gibbs free energy

Workflow Patterns

OER Overpotential

for ads in ["OH", "O", "OOH"]:
    opt = wf.add_task(geo_opt, structure=slab.output.structure,
                      system_name=f"*{ads}")
    frq = wf.add_task(freq, structure=opt.output.structure,
                      freeze_mode="layers", freeze_layers=4)
    gib = wf.add_task(gibbs_energy, energy=opt.output.energy,
                      frequencies=frq.output.frequencies, phase="adsorbed")

Convergence Test

for encut in [400, 500, 600, 700]:
    wf.add_task(single_point, structure=struct.output.structure,
                ENCUT=encut, system_name=f"ENCUT={encut}")

レビュー

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