Diffusion Analysis in a Pore (Bin Method)ΒΆ
The bin diffusion analysis needs the sampled object file using the bin diffusion routine
import porems as pms
import poreana as pa
mol = pms.Molecule(inp="data/benzene.gro")
sample = pa.Sample("data/pore_system_cylinder.obj", "data/traj_cylinder.xtc", mol, [])
sample.init_diffusion_bin("output/diff.h5")
sample.sample()
Finished frame 2001/2001...
The diffusion can be calculated through the entire pore
pa.diffusion.cui("output/diff.h5")
Diffusion axial: 0.741 10^-9 m^2s^-1
Diffusion radial: 648.838 10^-9 m^2 s^-1; Number of zeros: 41; Radius: 0.17
or binwise
pa.diffusion.bins("output/diff.h5")
By weighting the diffusion profile with the density profile, one can calculate an axial mean value
pa.diffusion.mean("output/diff.h5", "output/dens.h5")
Mean Diffusion axial: 1.131 10^-9 m^2s^-1