Linked cell neighbour list

Oct 13, 2025 by pynkocean.com 68 views

Introduction

In the realm of molecular dynamics simulations, the choice of pair interaction style and neighbour list management can significantly impact the accuracy and efficiency of the results. The LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) code, a widely used molecular dynamics simulator, has recently undergone a change that disallows the use of Newton pair 'on' with a full atoms list. This change, introduced in a pull request last year, has far-reaching implications for users who rely on this combination for their simulations. In this article, we will delve into the reasons behind this change, explore the consequences of this restriction, and discuss potential workarounds for users who require the use of Newton pair 'on' with a full neighbour list.

Background

For those unfamiliar with the terminology, Newton pair is a style of pair interaction that uses the Newtonian force law to compute the forces between atoms. This style is particularly useful for simulations that require high accuracy and precision, such as those involving complex molecular systems or long-range interactions. On the other hand, a full neighbour list refers to a data structure that keeps track of all atoms within a certain cutoff distance from each atom in the system. This list is essential for efficient neighbour searching and pair interaction computation.

The Change in LAMMPS

The change in LAMMPS that disallows the use of Newton pair 'on' with a full atoms list was introduced in a pull request last year. The reasoning behind this change is not explicitly stated in the pull request, but it is likely related to performance and memory usage considerations. By disallowing the use of Newton pair 'on' with a full atoms list, LAMMPS developers aim to improve the efficiency and scalability of the code, particularly for large-scale simulations.

Consequences of the Change

The change in LAMMPS has significant consequences for users who rely on the combination of Newton pair 'on' and a full neighbour list. One of the most notable consequences is the inability to use the Allegro/KK pair style, which requires both Newton pair 'on' and a full neighbour list. This pair style is particularly useful for simulations involving complex molecular systems or long-range interactions.

Workarounds

While the change in LAMMPS disallows the use of Newton pair 'on' with a full atoms list, there are potential workarounds for users who require this combination. One possible workaround is to use a different pair interaction style, such as the Verlet pair style, which does not require a full neighbour list. However, this may compromise the accuracy and precision of the results.

Another potential workaround is to use a different neighbour list management strategy, such as the Verlet neighbour list, which does not require a full neighbour list. However, this may also compromise the efficiency and scalability of the code.

Alternative Pair Styles

In the absence of Newton pair 'on' with a full neighbour list, users may need to consider alternative pair styles that do not require this combination. Some possible alternatives include:

Verlet pair style: This pair style uses the Verlet algorithm to compute the forces between atoms and does not require a full neighbour list.
SHAKE pair style: This pair style uses the SHAKE algorithm to constrain the bonds in a molecular system and does not require a full neighbour list.
RATTLE pair style: This pair style uses the RATTLE algorithm to constrain the bonds in a molecular system and does not require a full neighbour list.

Alternative Neighbour List Management Strategies

In addition to alternative pair styles, users may also need to consider alternative neighbour list management strategies that do not require a full neighbour list. Some possible alternatives include:

Verlet neighbour list: This neighbour list management strategy uses the Verlet algorithm to compute the neighbour list and does not require a full neighbour list.
Linked cell neighbour list: This neighbour list management strategy uses a linked cell data structure to compute the neighbour list and does not require a full neighbour list.
Grid neighbour list: This neighbour list management strategy uses a grid data structure to compute the neighbour list and does not require a full neighbour list.

Conclusion

Frequently Asked Questions

In this article, we will address some of the most frequently asked questions related to the change in LAMMPS that disallows the use of Newton pair 'on' with a full atoms list.

Q: What is the reason behind this change in LAMMPS?

A: The reason behind this change is not explicitly stated in the pull request, but it is likely related to performance and memory usage considerations. By disallowing the use of Newton pair 'on' with a full atoms list, LAMMPS developers aim to improve the efficiency and scalability of the code, particularly for large-scale simulations.

Q: What are the consequences of this change?

A: The change in LAMMPS has significant consequences for users who rely on the combination of Newton pair 'on' and a full neighbour list. One of the most notable consequences is the inability to use the Allegro/KK pair style, which requires both Newton pair 'on' and a full neighbour list.

Q: Are there any workarounds for this change?

A: Yes, there are potential workarounds for users who require the use of Newton pair 'on' with a full neighbour list. One possible workaround is to use a different pair interaction style, such as the Verlet pair style, which does not require a full neighbour list. Another possible workaround is to use a different neighbour list management strategy, such as the Verlet neighbour list, which does not require a full neighbour list.

Q: What are some alternative pair styles that do not require a full neighbour list?

A: Some possible alternative pair styles include:

Verlet pair style: This pair style uses the Verlet algorithm to compute the forces between atoms and does not require a full neighbour list.
SHAKE pair style: This pair style uses the SHAKE algorithm to constrain the bonds in a molecular system and does not require a full neighbour list.
RATTLE pair style: This pair style uses the RATTLE algorithm to constrain the bonds in a molecular system and does not require a full neighbour list.

Q: What are some alternative neighbour list management strategies that do not require a full neighbour list?

A: Some possible alternative neighbour list management strategies include:

Verlet neighbour list: This neighbour list management strategy uses the Verlet algorithm to compute the neighbour list and does not require a full neighbour list.
Linked cell neighbour list: This neighbour list management strategy uses a linked cell data structure to compute the neighbour list and does not require a full neighbour list.
Grid neighbour list: This neighbour list management strategy uses a grid data structure to compute the neighbour list and does not require a full neighbour list.

Q: How can I update my LAMMPS code to accommodate this change?

A: To update your LAMMPS code to accommodate this change, you will need to modify your input script to use a different pair interaction style or neighbour list management strategy. You can do this by changing the pair_style and neighbor keywords in your input script.

Q: Can I still use the Allegro/KK pair style with this change?

A: Unfortunately, no. The Allegro/KK pair style requires both Newton pair 'on' and a full neighbour list, which is no longer allowed in LAMMPS. You will need to use a different pair style or neighbour list management strategy to achieve similar results.

Conclusion

In this article, we have addressed some of the most frequently asked questions related to the change in LAMMPS that disallows the use of Newton pair 'on' with a full atoms list. We hope that this information has been helpful in understanding the implications of this change and in finding alternative solutions to achieve your simulation goals.