HOOMD simulation in real units

49 views
Skip to first unread message

Azamat Rizuan

unread,
Aug 13, 2021, 11:40:49 AMAug 13
to hoomd-users
Greetings,

I am planning to a slab simulation in HOOMD, using the trajectory from LAMMPS. To make it easier, I am using real units as LAMMPS. I have converted everything from LAMMPS to HOOMD and checked potentials in zero time step. Both are same. However, the issue now is time step. In LAMMPS, time step = 10 fs was working fine for me. However, it is giving error for me in HOOMD:
>>>
**ERROR**: Particle with unique tag 38318 is no longer in the simulation box.
Cartesian coordinates:
x: 1623.72 y: 579.309 z: 881.171
Fractional coordinates:
f.x: 8.61862 f.y: 3.39655 f.z: 0.814704
Local box lo: (-100, -100, -1400)
          hi: (100, 100, 1400)
Traceback (most recent call last):
  File "runfile.py", line 366, in <module>
    hoomd.run_upto(nsteps)
  File "/raid/codes/python3.7.6/lib/python3.7/site-packages/hoomd/__init__.py", line 242, in run_upto
    run(n_steps, **keywords);
  File "/raid/codes/python3.7.6/lib/python3.7/site-packages/hoomd/__init__.py", line 201, in run
    context.current.system.run(int(tsteps), callback_period, callback, limit_hours, int(limit_multiple));
RuntimeError: Error computing cell list
>>>

It is giving this after dt>1fs. I have used the different units to change unit of the time step to picoseconds and dt=0.01ps (which is equal to 10fs) was working fine to the same system. I am just wondered if it is some error from HOOMD or from my conversion?

Best,

Azamat

Joshua Anderson

unread,
Aug 23, 2021, 7:55:06 AMAug 23
to hoomd...@googlegroups.com
Azamat,

You do not specify the conversions factors you use with real units, so I do not have enough information to answer your question. I suspect you are missing one or more conversion factors, such as the conversion from femtoseconds to the self-consistent unit of time in this system of units.
------
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan
> --
> You received this message because you are subscribed to the Google Groups "hoomd-users" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to hoomd-users...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/hoomd-users/3b979778-f4d6-4e8b-b4f5-accc8d0e705en%40googlegroups.com.

Azamat Rizuan

unread,
Aug 26, 2021, 12:05:07 PMAug 26
to hoomd-users
Thanks, 
I solved this issue using the correct conversion factor for the unit of time.

Best,

Azamat
Reply all
Reply to author
Forward
0 new messages