Dear Lammps user,
Is ther anyway to measure the free volume for an amorphous polymer unit cell?
It is highly appreciated if you would also guide me about visualization of free volume. (Sorry if this is not related to the lammps)
Best
Musa
Dear Lammps user,
Is ther anyway to measure the free volume for an amorphous polymer unit cell?
that is not a well defined problem, since the the volume of an atom or a molecule is not well defined.
there are various approaches to approximate that, e.g. based on covalent radii or from the average volume per atom from a relaxed, densely filled simulation cell. you could then count the number of atoms (or atoms of a given type) and multiply those with the estimated per atom (or per atom type) volume and take the sum of those. the free volume is then the box volume minus the occupied volume.
It is highly appreciated if you would also guide me about visualization of free volume. (Sorry if this is not related to the lammps)
see my remark above. The VMD software has a “volmap” tool that can compute volumetric maps based on density or occupancy.
https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.3/ug/node156.html
https://www.ks.uiuc.edu/Research/vmd/plugins/volmapgui/
If you want to visualize the “free” volume, you can compute a density/occupancy map and write it to a file and then post-process the file by reversing the numbers, i.e. changing occupancy to 1-occupancy.
axel.
3 Likes