internscience 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)
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
cd ir-spectra-simulation
python ir_spectra_simulation.py CCO
XYZ（用户提供坐标文件）
cd ir-spectra-simulation
python ir_spectra_simulation.py /path/to/structure.xyz