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Molecular Dynamics

LAMMPS Patch Release 30 November 2020

December 1, 2020
21 min read
blog-LAMMPS-patch_30Nov2020.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 29 October 2020.

New features:

  • Added an electronic stopping fix to USER-MISC, James Stewart (SNL), Remi Dingreville (SNL), PR #2391
  • Added bond & angle styles gaussian, E. Voyiatzis (Royal DSM), PR #2440
  • Added Kokkos support for fix shake and forward comm on Device for fixes, Stan Moore (SNL), PR #2441
  • Added pair style spin/exchange/biquadratic, Julien Tranchida (SNL), PR #2410
  • Added molecule keyword to bond react to optionally force reaction to be inter- or intramolecular, Jacob Gissinger (NASA), PR #2467

Updates & Bugfixes:

  • Fixed issue with C library interface function lammps_gather_atoms, Richard Berger (Temple U), PR #2466
  • Add CMake code to download and compile a suitable version of libyaml in case it is not found locally, Axel Kohlmeyer (Temple U), PR #2476
  • Bugfixes in USER-MESONT, Maxim Shugaev (UVA), PR #2464
  • Fix memory bug in Kokkos KISS FFT, which led to crashes, Stan Moore (SNL), PR #2482
  • Separate cut planes by neigh skin for balance shift, Steve Plimpton (SNL), PR #2492
  • Patched neighbor history restarts, Joel Clemmer (SNL), PR #2424
  • Added missing LAMMPS_LIB_MPI flag to COUPLE-fortran2 example, PR #2495
  • Various fixes and updates for the KIM package, including support for KIM API v2.2.0, Yaser Afshar (UMN), Ryan S. Elliott (UMN), PR #2469, PR #2477, PR #2488
  • Updated bundled fmtlib to version 7.1.3, Axel Kohlmeyer (Temple U), PR #2451, PR #2487
  • Kokkos ReaxFF tweaks, Stan Moore (SNL), PR #2485
  • Preserve molecule templates when using "replicate", Axel Kohlmeyer (Temple U), PR #2462
  • molecule: use user-provided IDs in molecule files, Jacob Gissinger (NASA), PR #2450
  • Introduces constants into code base for energy and virial flags, Richard Berger (Temple U), PR #2481
  • Added support to the library interface to extract sublo, subhi, sublo_lambda, and subhi_lambda globals, Richard Berger (Temple U), Axel Kohlmeyer (Temple U), PR #2420
  • Added support to the library interface to extract universe_size, universe_rank, world_size, and world_rank settings, Axel Kohlmeyer (Temple U) PR #2420
  • Added support to the library interface to extract the newton_bond and newton_pair settings, Axel Kohlmeyer (Temple U), PR #2487
  • Added new unit tests, Axel Kohlmeyer (Temple U), Richard Berger (Temple U), PR #2487, PR #2420, PR #2478
  • Added support for -in none argument so that multi-partition runs can be launched from the library interface without an (initial or dummy) input file, Axel Kohlmeyer (Temple U), PR #2420
  • Reset invalid image flags on read_data, Axel Kohlmeyer (Temple U), Steve Plimpton (SNL), PR #2419
  • Bugfix for NEB, Tom D Swinburne (CNRS / Aix-Marseille University), PR #2486
  • Bugfixes for bond react, Jacob Gissinger (NASA), PR #2467
  • Update Kokkos library in LAMMPS to v3.2.1, Stan Moore (SNL), PR #2497
  • Kokkos EAM tweaks for V100, Stan Moore (SNL), PR #2436

Backward compatibility

  • for runs containing pair spin/exchange interactions, older restart files will no longer be compatible
  • Old restart files may not work if they saved neighbor/history data.
  • fix bond/react: updates map file section title from 'BondingIDs' to 'InitiatorIDs'. Old section title still works for backward compatibility, with a printed warning that it has been deprecated

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_30Nov2020.jpg
Molecular Dynamics

LAMMPS Patch Release 30 November 2020

December 1, 2020 21 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 29 October 2020.

New features:

  • Added an electronic stopping fix to USER-MISC, James Stewart (SNL), Remi Dingreville (SNL), PR #2391
  • Added bond & angle styles gaussian, E. Voyiatzis (Royal DSM), PR #2440
  • Added Kokkos support for fix shake and forward comm on Device for fixes, Stan Moore (SNL), PR #2441
  • Added pair style spin/exchange/biquadratic, Julien Tranchida (SNL), PR #2410
  • Added molecule keyword to bond react to optionally force reaction to be inter- or intramolecular, Jacob Gissinger (NASA), PR #2467

Updates & Bugfixes:

  • Fixed issue with C library interface function lammps_gather_atoms, Richard Berger (Temple U), PR #2466
  • Add CMake code to download and compile a suitable version of libyaml in case it is not found locally, Axel Kohlmeyer (Temple U), PR #2476
  • Bugfixes in USER-MESONT, Maxim Shugaev (UVA), PR #2464
  • Fix memory bug in Kokkos KISS FFT, which led to crashes, Stan Moore (SNL), PR #2482
  • Separate cut planes by neigh skin for balance shift, Steve Plimpton (SNL), PR #2492
  • Patched neighbor history restarts, Joel Clemmer (SNL), PR #2424
  • Added missing LAMMPS_LIB_MPI flag to COUPLE-fortran2 example, PR #2495
  • Various fixes and updates for the KIM package, including support for KIM API v2.2.0, Yaser Afshar (UMN), Ryan S. Elliott (UMN), PR #2469, PR #2477, PR #2488
  • Updated bundled fmtlib to version 7.1.3, Axel Kohlmeyer (Temple U), PR #2451, PR #2487
  • Kokkos ReaxFF tweaks, Stan Moore (SNL), PR #2485
  • Preserve molecule templates when using "replicate", Axel Kohlmeyer (Temple U), PR #2462
  • molecule: use user-provided IDs in molecule files, Jacob Gissinger (NASA), PR #2450
  • Introduces constants into code base for energy and virial flags, Richard Berger (Temple U), PR #2481
  • Added support to the library interface to extract sublo, subhi, sublo_lambda, and subhi_lambda globals, Richard Berger (Temple U), Axel Kohlmeyer (Temple U), PR #2420
  • Added support to the library interface to extract universe_size, universe_rank, world_size, and world_rank settings, Axel Kohlmeyer (Temple U) PR #2420
  • Added support to the library interface to extract the newton_bond and newton_pair settings, Axel Kohlmeyer (Temple U), PR #2487
  • Added new unit tests, Axel Kohlmeyer (Temple U), Richard Berger (Temple U), PR #2487, PR #2420, PR #2478
  • Added support for -in none argument so that multi-partition runs can be launched from the library interface without an (initial or dummy) input file, Axel Kohlmeyer (Temple U), PR #2420
  • Reset invalid image flags on read_data, Axel Kohlmeyer (Temple U), Steve Plimpton (SNL), PR #2419
  • Bugfix for NEB, Tom D Swinburne (CNRS / Aix-Marseille University), PR #2486
  • Bugfixes for bond react, Jacob Gissinger (NASA), PR #2467
  • Update Kokkos library in LAMMPS to v3.2.1, Stan Moore (SNL), PR #2497
  • Kokkos EAM tweaks for V100, Stan Moore (SNL), PR #2436

Backward compatibility

  • for runs containing pair spin/exchange interactions, older restart files will no longer be compatible
  • Old restart files may not work if they saved neighbor/history data.
  • fix bond/react: updates map file section title from 'BondingIDs' to 'InitiatorIDs'. Old section title still works for backward compatibility, with a printed warning that it has been deprecated

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