Boundary Regions in LAMMPS MD Simulation

[MechEngJordan]

Hi,

I'm working on a project using LAMMPS. I am very new to the software and find the documentation doesn't always answer the fundamental questions I have. I noted previous LAMMPS queries were posted on this forum, although I am from a mechanical/materials engineering background.

I am trying to build a substrate with three regions: one under NVE dynamics, an additional region acting as a thermostatic boundary (NVT dynamics) and a final fixed region (effectively the same idea as Goel et al. and Wang et al.).

My simulation is working well when the substrate is one region, all NVE; however, I am running into errors---possibly due to a misunderstanding of the syntax---when I try to add in these boundaries.

Any help on how to define these regions would be greatly appreciated.

 

[eljose79]

Hello,

Thank you for reaching out to us for assistance with your LAMMPS project. As a scientist with experience using LAMMPS, I would be happy to provide some guidance on how to define these different regions in your simulation.

First, it is important to note that LAMMPS has a very helpful user manual that includes detailed information on the syntax and commands used in the software. I would recommend referring to this manual when you encounter any issues or have questions about the software.

To define the three regions in your substrate, you will need to use the "region" command in your input script. This command allows you to specify the shape and size of a region in your simulation box. For example, to define the region with NVE dynamics, you can use the command:

region myregion block xlo xhi ylo yhi zlo zhi units box

This creates a rectangular region that extends from the specified x, y, and z coordinates in your simulation box. You can then use the "fix" command to assign NVE dynamics to this region:

fix 1 myregion nve

Similarly, you can define the region with NVT dynamics and assign the corresponding fix command to it. As for the fixed region, you can simply use the "fix" command to set the atoms in this region as immobile:

fix 2 fixedatoms setforce 0.0 0.0 0.0

I would also recommend checking out the LAMMPS mailing list and forum for more specific examples and tips on defining regions in your simulations.

I hope this helps and please let me know if you have any further questions or concerns. Best of luck with your project!