Boundary Regions in LAMMPS MD Simulation

In summary, the conversation involves a person seeking help with defining three regions in their LAMMPS simulation: one with NVE dynamics, one with NVT dynamics, and one fixed region. The expert recommends using the "region" and "fix" commands in the input script and suggests referring to the LAMMPS user manual and online resources for more specific examples and guidance.
  • #1
MechEngJordan
17
0
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.
 
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  • #2


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!
 

FAQ: Boundary Regions in LAMMPS MD Simulation

1. What is the purpose of defining boundary regions in LAMMPS MD simulation?

The purpose of defining boundary regions in LAMMPS MD simulation is to specify the boundaries or edges of the simulated system. This allows for the accurate calculation of forces and interactions between atoms within the simulation, as well as controlling the movement and behavior of atoms near the boundaries.

2. How are boundary regions defined in LAMMPS MD simulation?

Boundary regions in LAMMPS MD simulation are defined by using the "boundary" command in the input script. This command allows the user to specify the dimensions and shape of the simulation box, as well as any periodic boundary conditions that may be applied.

3. What types of boundary conditions can be applied in LAMMPS MD simulation?

The most commonly used boundary conditions in LAMMPS MD simulation are periodic and non-periodic. Periodic boundary conditions simulate an infinite system by wrapping atoms around the simulation box, while non-periodic boundary conditions allow for a fixed number of atoms within the simulation box. Additionally, some specialized boundary conditions such as reflective or shrink-wrapped may also be available in LAMMPS.

4. Can boundary regions be changed during a LAMMPS MD simulation?

Yes, boundary regions can be changed during a LAMMPS MD simulation by using the "change_box" command in the input script. This allows for the simulation box to be expanded, contracted, or shifted in any direction during the simulation, which can be useful for studying phase transitions or other structural changes in the system.

5. How do boundary regions affect the accuracy of LAMMPS MD simulation results?

The accuracy of LAMMPS MD simulation results can be greatly affected by the choice of boundary regions. Improperly defined or changing boundary regions can lead to artifacts and errors in the simulation results, as well as affecting the behavior of atoms near the boundaries. It is important to carefully consider and validate the choice of boundary regions in order to obtain accurate and meaningful results from the simulation.

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