Diameter data overwritten in trajectory.gsd

[Damienfg]

Hi,

I'm using HOOMD to simulate the behavior of large spheres (colloids) in a bath of smaller spheres (solvent). A DPD framework is used along with a Lennard-Jones potential. I specified a diameter of 1.2 for the colloids and 0.08 for the solvent particles.

The simulation runs correctly, and I can read the outcome (trajectory.gsd) in Ovito.

However, using Ovito is annoying because I have to specify the diameters of the two types of particles every time I read the GSD file with Ovito. If my understanding is correct, this is because Ovito reads radius, not diameter.

Before switching definitely to another viewer like ChimeraX, I started examining the content of my GSD file to see if I could change something to make Ovito read a radius.

I noticed that the diameters I specified in my HOOMD Python code are overwritten in the trajectory.gsd file. All the diameter data are set to 1.0 (not 1.2 and 0.08).

I must be doing something wrong, but I don't know what.

Here is the part of the code dedicated to the gsd outcome :

# 🔹 Configuration de la sortie GSD
gsd_writer = hoomd.write.GSD(
    filename="/media/damien/T7/Simulation/Colloids/Final/LJDPD/trajectory.gsd",
    trigger=hoomd.trigger.Periodic(2000),
    mode='wb'
)
sim.operations.writers.append(gsd_writer)

I’m not copying the entire code to keep this message clear, but I can if necessary.

Many thanks for your help.

Damien

[joaander]

Add:

gsd.write_diameter = True

to include the diameters in your output.