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Molecular Dynamics

LAMMPS Patch Release 14 May 2021

May 17, 2021
17 min read
blog-LAMMPS-patch_14May2021.jpg

LAMMPS Patch Release Overview

What is LAMMPS used for?

LAMMPS is a classical molecular dynamics (MD) code that models ensembles of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, solid-state (metals, ceramics, oxides), granular, coarse-grained, or macroscopic systems using a variety of interatomic potentials (force fields) and boundary conditions. It can model 2D or 3D systems with only a few particles up to millions or billions.

LAMMPS can run on single processor laptops or desktops, but is designed for parallel computers using message-passing techniques and a spatial-decomposition of the simulation domain. This includes shared-memory boxes and distributed-memory clusters and supercomputers. Many of its models have versions that provide accelerated performance on CPUs, GPUs, and Intel Xeon Phis. The code is designed to be easy to modify or extend with new functionality.



Interested in getting faster results?
Learn more about LAMMPS Certified GPU Workstations and Servers starting at $4,300


Changes since the patch release 8 April 2021:

  • New package USER-PACE which provides a new pair style pace computing interactions using the Atomic Cluster
    Expansion (ACE) (Yury Lysogorskiy and collaborators at ICAMS, Ruhr-Uni Bochum) PR #2699
  • New Package USER-BROWNIAN for Brownian dynamics time integration of point and extended particles plus updates for fix propel/self (Sam Cameron, U Bristol) PR #2511
  • New Package USER-MDI to enable client/server mode coupling of LAMMPS with other codes using the MolSSI Driver Interface (MDI) (Taylor Barnes, MolSSI) PR #2611
  • New fix style "charge/regulation" which implements Monte Carlo sampling of charge regulation (Tine Curk, Northwestern U and Jiaxing Yuan, Shanghai Jiao Tong U) PR #2585
  • New generalized DPD pair styles: dpd/ext and dpd/ext/tstat (Martin Svoboda, Karel Sindelka, and Martin Lisal, ICPF) PR #2710
  • Faster and more flexible support for multi style neighbor lists (Joel Clemmer, SNL) PR #2536
  • New pair style hybrid/scaled that allows combining contributions from different pair styles with constant or variable scaling factors (Axel Kohlmeyer, Temple U) PR #2702
  • Updated version of pair style bop with bugfixes and performance improvements (Xiaowang Zhou, SNL) PR #2750, PR #2753
  • New base class Command that all command styles are now derived from instead of the Pointers class (Axel Kohlmeyer, Temple U) PR #2707
  • GPU package version of pair style lj/smooth (Gurgen Melikyan, HSE University) PR #2706
  • Update of the bundled Kokkos library to version 3.4.0 (Stan Moore, SNL and the Kokkos developers) PR #2733
  • Support for atom style spin in the KOKKOS package (Julien Tranchida, Stan Moore, and Svetoslav Nikolov, SNL) PR #2693
  • New clang-format configuration file in src tree. All files in that tree are prepared so that clang-format can be applied without destroying functionality. (Axel Kohlmeyer, Temple U) PR #2762
  • Refactoring of core LAMMPS code and packages to increase code reuse and readability, simplify text parsing, improve thread safety (Richard Berger and Axel Kohlmeyer, Temple U) PR #2704, PR #2719, PR #2727, PR #2738, PR #2749
  • Bugfixes and updates for the GPU package addressing issues caused by the changes/improvements in PR #2603 (Mike Brown, Intel Corp., Trung Nguyen, Northwestern U, and Richard Berger, Temple U) PR #2711, PR #2720, PR #2723, PR #2744, PR #2745, PR #2756
  • More unit tests for MPI load balancing and file operations (Richard Berger and Axel Kohlmeyer, Temple U) PR #2642, PR #2725
  • Scripts to support building LAMMPS and its documentation on systems without direct internet access (Richard Berger, Temple U) PR #2742
  • Various small bug fixes, coding style and formatting updates (multiple authors) PR #2703, PR #2705, PR #2712, PR #2713, PR #2714, PR #2715, PR #2717, PR #2721, PR #2722, PR #2724, PR #2726, PR #2737, PR #2739, PR #2741, PR #2743, PR #2748, PR #2756, PR #2758, PR #2760, PR #2761, PR #2765, PR #2769

Backward compatibility notes:

  • using comm_modify multi now requires to also use neighbor multi. In case the new neighbor multi functionality causes problems, it is possible to revert to the previous implementation with neighbor multi/old. In that case comm_modify multi/old and comm_modify cutoff/multi/old need to be used for enabling and customizing multi-cutoff ghost atom communication.
  • binary restart files containing data for pair style coul/cut will be incompatible due to bugfixes (but they were broken anyway)
  • external packages that add command styles will have to be adapted to the changes to the class topology in PR #2707

This release has 2 assets:

  • Source code (zip)
  • Source code (tar.gz)

Visit the release page to download them.


About LAMMPS

LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) a classical molecular dynamics simulation code designed to run efficiently on parallel computers. It was developed at Sandia National Laboratories, a US Department of Energy facility, with funding from the DOE. It is an open-source code, distributed freely under the terms of the GNU Public License (GPL).


Have any questions about LAMMPS or other applications for molecular dynamics? Contact Exxact Today

Free Resources

Browse our whitepapers, e-books, case studies, and reference architecture.

Explore
blog-LAMMPS-patch_14May2021.jpg
Molecular Dynamics

LAMMPS Patch Release 14 May 2021

May 17, 2021 17 min read

LAMMPS Patch Release Overview

What is LAMMPS used for?

LAMMPS is a classical molecular dynamics (MD) code that models ensembles of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, solid-state (metals, ceramics, oxides), granular, coarse-grained, or macroscopic systems using a variety of interatomic potentials (force fields) and boundary conditions. It can model 2D or 3D systems with only a few particles up to millions or billions.

LAMMPS can run on single processor laptops or desktops, but is designed for parallel computers using message-passing techniques and a spatial-decomposition of the simulation domain. This includes shared-memory boxes and distributed-memory clusters and supercomputers. Many of its models have versions that provide accelerated performance on CPUs, GPUs, and Intel Xeon Phis. The code is designed to be easy to modify or extend with new functionality.



Interested in getting faster results?
Learn more about LAMMPS Certified GPU Workstations and Servers starting at $4,300


Changes since the patch release 8 April 2021:

  • New package USER-PACE which provides a new pair style pace computing interactions using the Atomic Cluster
    Expansion (ACE) (Yury Lysogorskiy and collaborators at ICAMS, Ruhr-Uni Bochum) PR #2699
  • New Package USER-BROWNIAN for Brownian dynamics time integration of point and extended particles plus updates for fix propel/self (Sam Cameron, U Bristol) PR #2511
  • New Package USER-MDI to enable client/server mode coupling of LAMMPS with other codes using the MolSSI Driver Interface (MDI) (Taylor Barnes, MolSSI) PR #2611
  • New fix style "charge/regulation" which implements Monte Carlo sampling of charge regulation (Tine Curk, Northwestern U and Jiaxing Yuan, Shanghai Jiao Tong U) PR #2585
  • New generalized DPD pair styles: dpd/ext and dpd/ext/tstat (Martin Svoboda, Karel Sindelka, and Martin Lisal, ICPF) PR #2710
  • Faster and more flexible support for multi style neighbor lists (Joel Clemmer, SNL) PR #2536
  • New pair style hybrid/scaled that allows combining contributions from different pair styles with constant or variable scaling factors (Axel Kohlmeyer, Temple U) PR #2702
  • Updated version of pair style bop with bugfixes and performance improvements (Xiaowang Zhou, SNL) PR #2750, PR #2753
  • New base class Command that all command styles are now derived from instead of the Pointers class (Axel Kohlmeyer, Temple U) PR #2707
  • GPU package version of pair style lj/smooth (Gurgen Melikyan, HSE University) PR #2706
  • Update of the bundled Kokkos library to version 3.4.0 (Stan Moore, SNL and the Kokkos developers) PR #2733
  • Support for atom style spin in the KOKKOS package (Julien Tranchida, Stan Moore, and Svetoslav Nikolov, SNL) PR #2693
  • New clang-format configuration file in src tree. All files in that tree are prepared so that clang-format can be applied without destroying functionality. (Axel Kohlmeyer, Temple U) PR #2762
  • Refactoring of core LAMMPS code and packages to increase code reuse and readability, simplify text parsing, improve thread safety (Richard Berger and Axel Kohlmeyer, Temple U) PR #2704, PR #2719, PR #2727, PR #2738, PR #2749
  • Bugfixes and updates for the GPU package addressing issues caused by the changes/improvements in PR #2603 (Mike Brown, Intel Corp., Trung Nguyen, Northwestern U, and Richard Berger, Temple U) PR #2711, PR #2720, PR #2723, PR #2744, PR #2745, PR #2756
  • More unit tests for MPI load balancing and file operations (Richard Berger and Axel Kohlmeyer, Temple U) PR #2642, PR #2725
  • Scripts to support building LAMMPS and its documentation on systems without direct internet access (Richard Berger, Temple U) PR #2742
  • Various small bug fixes, coding style and formatting updates (multiple authors) PR #2703, PR #2705, PR #2712, PR #2713, PR #2714, PR #2715, PR #2717, PR #2721, PR #2722, PR #2724, PR #2726, PR #2737, PR #2739, PR #2741, PR #2743, PR #2748, PR #2756, PR #2758, PR #2760, PR #2761, PR #2765, PR #2769

Backward compatibility notes:

  • using comm_modify multi now requires to also use neighbor multi. In case the new neighbor multi functionality causes problems, it is possible to revert to the previous implementation with neighbor multi/old. In that case comm_modify multi/old and comm_modify cutoff/multi/old need to be used for enabling and customizing multi-cutoff ghost atom communication.
  • binary restart files containing data for pair style coul/cut will be incompatible due to bugfixes (but they were broken anyway)
  • external packages that add command styles will have to be adapted to the changes to the class topology in PR #2707

This release has 2 assets:

  • Source code (zip)
  • Source code (tar.gz)

Visit the release page to download them.


About LAMMPS

LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) a classical molecular dynamics simulation code designed to run efficiently on parallel computers. It was developed at Sandia National Laboratories, a US Department of Energy facility, with funding from the DOE. It is an open-source code, distributed freely under the terms of the GNU Public License (GPL).


Have any questions about LAMMPS or other applications for molecular dynamics? Contact Exxact Today

Free Resources

Browse our whitepapers, e-books, case studies, and reference architecture.

Explore