Compute vibrational spectra from MD trajectory — power spectrum (velocity autocorrelation) or IR (dipole autocorrelation) via MLatom.
Use this skill when the user has an MD trajectory and wants:
/tmp/chemclaw/power_spectrum.png/tmp/chemclaw/ir_spectrum.png — IR spectrum（--spectrum ir，需轨迹含 dipole）conda create -n spec python=3.12 -y
conda activate spec
conda install -c conda-forge xtb -y
cd md-vib-spectra-simulation
pip install -r requirements.txt
python power_spectrum_simulation.py CCO --run-md --spectrum ps --time 20 --temp 300 --md-dt 0.5 --autocorr 8 --zeropad 16
xtb；requirements.txt 已涵盖主要依赖。--run-md 与 IR/Raman 相同，需系统可用的 xtb（conda-forge）。cd md-vib-spectra-simulation
python power_spectrum_simulation.py ethanol_traj.h5 --dt 0.5
cd md-vib-spectra-simulation
python power_spectrum_simulation.py assets/ethanol_traj.xyz --vxyz assets/ethanol_traj.vxyz --dt 0.5
cd md-vib-spectra-simulation
# h5md 来自 AIQM1/MNDO 等有 dipole 的方法
python power_spectrum_simulation.py ethanol_traj.h5 --spectrum ir
# xyz + vxyz + dp（每行 dx dy dz）
python power_spectrum_simulation.py traj.xyz --vxyz traj.vxyz --dp traj.dp --spectrum ir
# 同时输出 power spectrum 与 IR
python power_spectrum_simulation.py ethanol_traj.h5 --spectrum both
cd md-vib-spectra-simulation
# GFN2-xTB（可直接算 power spectrum）
python power_spectrum_simulation.py CCO --run-md --time 1000 --temp 300 --md-dt 0.5
# GFN2-xTB（有 dipole，可算 IR + power spectrum）
python power_spectrum_simulation.py CCO --run-md --spectrum both --time 500
cd md-vib-spectra-simulation
python power_spectrum_simulation.py traj.h5 \
--dt 0.5 \
--autocorr 1024 \
--zeropad 1024 \
--lb 0 --ub 10000 \
--output /tmp/chemclaw/power_spectrum.png
Note: --autocorr must be ≤ trajectory length (in fs). For short trajectories (e.g. 60 fs), use --autocorr 32 --zeropad 64.
GFN2-xTB。