Atoms lost using periodic boundary conditions in LIGGGHTS v3.8.0 with triclinic box

Submitted by rangr1 on Fri, 07/27/2018 - 10:55

I am setting up a single particle simulation with periodic boundary conditions (PBC) in LIGGGHTS-PUBLIC v3.8.0 and find that the atom is getting lost once it crosses the boundary for a triclinic box. This does not happen when I use LIGGGHTS-PUBLIC v3.5.0 or v3.4.1 for instance.

Please take a look at the input script attached that shows the behaviour described above. This atom is not lost if "block" is used instead of "prism" in my input script. I don't understand why this is happening, and perhaps it may be a bug.

Plain text icon LIGGGHTS input script579 bytes
arnom's picture

arnom | Wed, 08/08/2018 - 11:37

Triclinic is a feature we normally don't use at DCS (incl. our customers). Because of that we probably won't look into this issue any time soon. If anybody has a fix for the issue please post it here or submit a pull request and we'll be happy to include it in the next release.

Thanks for your understanding,

DCS team member & LIGGGHTS(R) core developer

Franzzzzzzzz | Wed, 01/22/2020 - 02:22

If anyone's still interested, this comes from a bug in the src/domain.cpp file, with the line initialising prd_lambda to zeros instead of one. So line 144 of domain.cpp in commit 1230dbd should read:
prd_lamda[0] = prd_lamda[1] = prd_lamda[2] = 1.0;

jagan1mohan | Sun, 03/08/2020 - 23:24

Hello Franzzzz,

Greetings. I'm having an orthogonal periodic cube filled with particles. When I use nve/sphere in LIGGGHTS, particles stay inside and move across periodic boundary(s) as expected. When I convert box into triclinic, either by "0 0 0 XY XZ YZ" header or "change_box", I loose all particles within few time steps when I use nve/sphere. Do you know how to address this situation? I want to use this triclinic box to apply shear on XY plane but I'm unable to hold particles within even without any applied forces.

Thank you,
Jagan Mohan.

jagan1mohan | Wed, 03/11/2020 - 02:19

Hello Matt, Thanks for your reply. The output log when I run LIGGGHTS on my system gives following information.

LIGGGHTS (Version LIGGGHTS-PUBLIC 3.8.0, compiled 2019-12-06-20:21:52 by jb, git commit ce1931e377a2945e3fa25dae0eebc1f697009a32)

Is this the latest version? How to update it to latest version?

Thank you,
Jagan Mohan.

jagan1mohan | Sat, 06/06/2020 - 22:07

Hello Matt, Thanks for your reply. How do we come to know when LIGGGHTS is updated? Is there a reminder email / forum? Perhaps, using the latest version is always better.

Thank you,
Jagan Mohan.

mschramm | Sun, 06/07/2020 - 05:47

On github you can "watch" a repository. Then anytime an update happens, you will get an email.

As for updates on a schedule, I don't believe there is one. As far as I know, the public users just hope that an update will eventually happen and rejoice when one happens.

mofazli | Thu, 08/06/2020 - 12:02

Dear Rangr1,
Did you want to impose the shear flow for that periodic box (Lees-Edwards Boundary Condition) using the triclinic box? If so, could you please tell us how did you that?