MDAnalysis Workflow

Example using DielectricSpectrum with MDAnalysis.

This example shows that the refactored DielectricSpectrum class still works exactly as before, maintaining backward compatibility.

import MDAnalysis as mda
from spectrumkit import DielectricSpectrum

Load your trajectory

u = mda.Universe("water.tpr", "water.trr")

Select atoms (e.g., all atoms in the system)

atomgroup = u.select_atoms("all")

Create DielectricSpectrum analysis This works exactly as before - the dipole calculation and spectrum calculation are still integrated in the class

analysis = DielectricSpectrum(
    atomgroup=atomgroup,
    temperature=300,
    output_prefix="water",
    segs=20,
    bins=200,
    binafter=20,
    nobin=False,
)

Run the analysis

analysis.run()

<spectrumkit.dielectricspectrum.DielectricSpectrum object at 0x7f34b3709e80>

Access results

print(f"Average volume: {analysis.results.V:.2f} Ų")
print(f"Number of frames: {len(analysis.results.P)}")
print(f"Frequency points: {len(analysis.results.nu)}")
print(f"Frequency range: {analysis.results.nu[0]:.4f} - "
      f"{analysis.results.nu[-1]:.4f} THz")

Average volume: 15443.71 Ų
Number of frames: 101
Frequency points: 3
Frequency range: 0.0000 - 1.0000 THz

Save results

analysis.save()

print("\nAnalysis complete!")
print(f"Results saved with prefix: {analysis.output_prefix}")

Analysis complete!
Results saved with prefix: water_