Regarding Calculation of Nematic order parameter from LAMMPS data using Freud software

[SAHIRE AZAM ANSARY]

Hi,

    I am using LAMMPS for MD of liquid crystal systems. From LAMMPS I get a dump file which has position and quaternion values. I used

# Script to compute nematic order parameter using freud:
import freud
import numpy as np

quaternions = np.genfromtxt("output_file", skip_header=9, max_rows=1000)

u = np.array([0, 0, 1])
nematic = freud.order.Nematic(u=u)
nematic.compute(quaternions)

print("Nematic order parameter:", nematic.order)
print("Nematic director:", nematic.director)
print("Nematic tensor:", nematic.nematic_tensor)

 

to find a nematic order parameter. Here I attach a dump file. I started my MD simulation from Simple cubic lattice structure. so if I find the first frame of the dump file I should get  order parameter value 1 or near 1.But  I did not get it. Why did this happen?

[Tommy Waltmann]

Hi Sahireaza,

Nematic order is a type of orientational order, not a type of translational order. The fact that your system begins in a simple cubic crystal does not mean that it should have perfect orientational order.

If you want to find translational ordering, there are many other ways to use freud to accomplish that goal. If you want to use an order parameter, the Steinhardt order parameters (https://freud.readthedocs.io/en/latest/modules/order.html#freud.order.Steinhardt) can help. Another way would be to compute a radial distribution function (https://freud.readthedocs.io/en/latest/modules/density.html#freud.density.RDF) and compare to the computed RDF of the RDF of the perfect crystal.

Try these methods and let me know if they work for you!

Best,

Tommy

[Tommy Waltmann]

That last sentence should read "Another way would be to compute a radial distribution function and compare the computed RDF to the RDF of the perfect crystal."

[Bradley Dice]

Sahire,

Just wanted to add this note in reply to your other email to me:

For the "u" argument, you need to use the molecular director of your particle. This is the axis about which the particle has rotational symmetry. The orientation quaternions act on this vector when computing the nematic order parameter. It might be along the z-axis like [0, 0, 1] or along the x-axis like [1, 0, 0] or along the y-axis like [0, 1, 0], or any other vector. It just depends on how your particles were specified, which only you will know. Try using the x-axis [1, 0, 0] or y-axis [0, 1, 0] and see if that fixes your problem.

Best,

Bradley