Those existed in v2 because the API was not expressive or performant enough for users to implement their own workflows using them. This is fixed in v3, so you can now implement workflows in a few lines of Python code that integrate cleanly with your workflow engine, job submission system, or anything else.
For example, run_upto is:
sim.run(max(0, final_timestep - sim.timestep))
A wall time limit can be achieved with (made possible by a minimal overhead run() call):
while time.time() < end_time - buffer:
Additionally, all operations are pickleable so if you want you can save them to a file and reload it when you continue your job.
I plan to include cover restartable jobs in a tutorial at some point. This tutorial will no longer recommend one script with multiple stages for workflows. Instead, it will use signac-flow (which many HOOMD users find convenient) to drive the different stages of the simulation: https://docs.signac.io/projects/flow/en/latest/
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan
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