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Prepare SIESTA molecular-dynamics task inputs from a user-provided structure and MD controls. Use when the user needs finite-temperature trajectories with explicit ensemble, timestep, and thermostat controls.
Codex または Claude でインストール この Prompt をコピーして Codex、Claude、または他のアシスタントに貼り付けると、Skill ページを確認してインストールできます。
SOC 職業分類に基づく
A versatile CLI tool for converting molecular file formats, generating 3D atomic coordinates from SMILES, rendering 2D chemical structure images, and preparing or extracting structures for computational workflows. USE WHEN you need to convert between chemical file formats (e.g., xyz, pdb, mol, smi, gjf), generate 3D structures from SMILES using `--gen3d`, render molecule images (PNG/SVG), or extract geometries from simulation logs to build new inputs.
Prepare and explain xTB semiempirical quantum-chemistry workflows for single-point energy, forces, charges, dipole, geometry optimization, and molecular dynamics. Use when the user asks for xTB calculations directly, or wants to use xTB through Python/ASE/dpdata bridges while keeping xTB as the primary method rather than as an ASE-only backend.
Run Shell commands as computational jobs, on local machines or HPC clusters, through Shell, Slurm, PBS, LSF, Bohrium, etc. USE WHEN the user needs to submit batch jobs to a cluster, run commands on a remote server, execute tasks via job schedulers (Slurm, PBS, LSF), or safely run long-term/background shell commands that require state tracking and auto-recovery.
A standardized CLI wrapper for RDKit 3D/2D conformer generation that samples multiple conformers per molecule (ETKDGv3, default 10), optimizes each with a force field (MMFF94s/UFF), keeps the lowest-energy conformer, automatically falls back to 2D layout on total embedding failure with a printed warning, and writes results to SDF or XYZ format. USE WHEN you need to generate 3D (or 2D fallback) molecular geometries from SMILES datasets (.csv/.smi) for downstream tasks such as docking, visualization, or 3D-descriptor computation.
A standardized CLI wrapper for RDKit molecular featurization workflows that handles physicochemical descriptor computation (outputs .csv) and molecular fingerprint extraction (outputs .npy or .csv), with built-in SMILES validation. USE WHEN you need to compute RDKit molecular descriptors or fingerprints from SMILES datasets (.csv/.smi), or when you want to list all available descriptor names and presets.
Configure ASE GPAW calculator adapter settings for ASE workflows. Use when ASE workflow tasks require GPAW backend setup including mode, k-point, convergence, and restart policies.
| name | md |
| description | Prepare SIESTA molecular-dynamics task inputs from a user-provided structure and MD controls. Use when the user needs finite-temperature trajectories with explicit ensemble, timestep, and thermostat controls. |
| compatibility | Requires a user-provided structure, compatible pseudopotentials, and runnable SIESTA environment. |
| license | MIT |
| catalog-hidden | true |
| metadata | {"author":"qqgu","version":"0.1.0","repository":"https://gitlab.com/siesta-project/siesta"} |
This skill prepares MD tasks only.
It should generate:
It should not submit or execute jobs.
NVE/NVT/NPT)dpdisp-submit if execution is requested