Calculating nematic order parameter from GSD file

[annaashki]

Hi all,

I'm new to using freud so this is probably an extremely straightforward thing to do but I just can't figure it out. What I'm trying to do is get a general idea of how to calculate the nematic order parameter for each frame of the GSD trajectory file produced by a HOOMD simulation. The relevant bits of code are:
traj = gsd.hoomd.open('C:\Users\...') - this is the path to the file. When I try to input 'rb', as in the example codes on readthedocs,
the output is 'Invalid mode: rb' - this might be the source of the problem?

After this I try: axes = [[1, 0, 0], [0, 1, 0], [0, 0, 1], [1, 1, 0], [1, 0, 1], [0, 1, 1], [1, 1, 1]]
for frame in traj:
for ax in axes:
nop = freud.order.Nematic(ax)
nop.compute(system=frame)
print(f"For axis {ax}, the value of the order parameter is {nop.order:0.3f}.")#

which returns 'compute() takes exactly 1 positional argument, 0 given'. Alternatively, I have tried to run
for i, frame in traj:
... positions[i]=frame.particles.position
... orientations[i]=frame.particles.orientation - this yields 'cannot unpack non-iterable Frame object'.

If anyone could give me a hint with this, I'd appreciate it a lot!

[joaander]

Use mode='r'.

This is documented in the GSD changelog and documentation for open.

[annaashki]

Thank you, this has worked -- the other errors remain unchanged so the type wasn't causing them. Do you have any idea what might be?

[tommy-waltmann]

The compute method of the Nematic class takes one argument which is the orientations, it does not take a trajectory frame. This is stated in the documentation

[annaashki]

Fixed now, thank you!