ir-spectra-simulation

# IR Spectra Simulation Skill ## When to use this Use this skill when the user provides a **SMILES** or **XYZ file** (coordinates) and wants: - Optimized geometry - Theoretically calculated IR spectrum in a summarized table - Quick overview of simulated IR - Publication-ready image file ## Inputs - **SMILES string** (e.g. CCO for ethanol) or **XYZ file path** (necessary) - Experimental IR spectrum file (optional, .txt format) ## Outputs - `/tmp/chemclaw/optimized_geometry.md` - `/tmp/chemclaw/theoretical_ir.md` - `/tmp/chemclaw/theoretical_ir.png` - `/tmp/chemclaw/exp_ir.png` (可选，提供实验数据时) - `/tmp/chemclaw/comparison_ir.png` (可选，提供实验数据时) ## New environment (from zero) ```bash conda create -n spec python=3.12 -y conda activate spec conda install -c conda-forge xtb -y # macOS 必装（MLatom 内建 xTB 为 Linux 版） pip install mlatom numpy matplotlib pyscf geometric rdkit cd ir-spectra-simulation python ir_spectra_simulation.py CCO # optional: python ir_spectra_simulation.py /path/to/structure.xyz # optional: python ir_spectra_simulation.py CCO exp.txt ``` - 请在 skill 目录内执行脚本（`cd ir-spectra-simulation`）。 - macOS 若仍误用 MLatom 内建 Linux 版 xTB，可确保 `which xtb` 指向 conda 的 `xtb`（必要时 `export PATH="$CONDA_PREFIX/bin:$PATH"`）。 ## How to run（已装好环境时） ### SMILES ```bash cd ir-spectra-simulation python ir_spectra_simulation.py CCO ``` ### XYZ（用户提供坐标文件） ```bash cd ir-spectra-simulation python ir_spectra_simulation.py /path/to/structure.xyz ```