Periodically save particle positions

[Pavel Baláž]

Hello,

I am trying to save all particles positions into a gsd file during a simulation after each num_out steps.
As I understood setting dynamic=["properties"] in hoomd.write.GSD should be enough. I used this code:

logger = hoomd.logging.Logger()
logger.add(thermodynamic_properties)
logger.add(sim, quantities=["timestep", "walltime"])

gsd_writer = hoomd.write.GSD(filename=log_file,
                              trigger=hoomd.trigger.Periodic(num_out),
                              mode="wb",
                              dynamic=["property"],
                              filter=hoomd.filter.Null())
sim.operations.writers.append(gsd_writer)
gsd_writer.log = logger

sim.run(num_steps)

Unfortunately, when I read the log file and look for traj[i].particles.position it is empty. Do you have any idea where might be the problem?

Thanks, Pavel

[Joshua Anderson]

Pavel,

You are selecting no particles for output with `filter=hoomd.filter.Null()`. Use `filter=hoomd.filter.All()` to include all particles in the GSD file.

------

Joshua A. Anderson, Ph.D.

Research Area Specialist, Chemical Engineering, University of Michigan

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[Pavel Baláž]

Dear Joshua,

thank you. Probably I misunderstood the meaning of that filter. Now it works.

Best,

Pavel

[Joshua Anderson]

Pavel,

It looks like you copied that from the logging example where it demonstrates how to make a GSD file that only contains the log quantities and no particles: 

https://hoomd-blue.readthedocs.io/en/v3.3.0/tutorial/02-Logging/01-Logging-to-a-GSD-file.html#Writing-log-quantities-to-a-GSD-file

The following tutorial shows how to combine particles and logged quantities in the same file:

https://hoomd-blue.readthedocs.io/en/v3.3.0/tutorial/02-Logging/02-Saving-Array-Quantities.html#Writing-per-particle-quantities-to-a-GSD-file

------

Joshua A. Anderson, Ph.D.

Research Area Specialist, Chemical Engineering, University of Michigan

To view this discussion on the web visit https://groups.google.com/d/msgid/hoomd-users/234176ee-5f55-42dd-8c10-850c7a8806a7n%40googlegroups.com.