LAMMPS Patch Release 1 February 2019

LAMMPS is a highly flexible, highly scalable software suite for molecular dynamics developed by Sandia National Laboratories. Listed below is their newest patch release, as of February 1, 2019.

New LAMMPS Patch Release Update

Changes since stable release 4 January 2018:

• new package USER-YAFF providing styles for force fields using QuickFF used for simulation of MOFs (Steven Vandenbrande, Ghent University): PR #1297 and PR #1301
• removal of moltemplate distribution from LAMMPS. Instead detailed installation instructions are provided to install via pip or through download of the up-to-date version from moltemplate.org (Andew Jewett, Axel Kohlmeyer): PR #1270
• added soft versions of CLASS2 pair style to USER-FEP, consolidation of documentation of all such pair styles, improved documentation of approximations for tail collection (Evangelos Voyatsis, Agilio Padua, Axel Kohlmeyer): PR #1302 (combines closed PRs #1300 #1293 #1289 and addresses issue #1269)
• support writing data of computes and fixes with arbitrary number of columns to NetCDF format dump files (Lars Pastewka, University of Freiburg): PR #1303
• add support for using fix qeq/shielded with pair_style reax/c (Axel Kohlmeyer, Temple U): PR #1310
• fix bond/react bugfixes and enhancements: reaction limit and reaction constraints (Jacob Gissinger, U Colorado): PR #1298, PR #1292, PR #1288, PR #1286, PR #1275
• bugfixes for issues #1294, #1284, #1283 (Axel Kohlmeyer, Temple U): PR #1282
• bugfixes for extraneous or missing callbacks to the Atom class (Axel Kohlmeyer, Temple U): PR #1311
• bugfixes for virial calculation of improper styles fourier and umbrella (Steven Vandenbrande, Ghent University), PR #1291
• bugfix for wrong dimension setting in the extract function for USER-DRUDE pair styles (Agilio Padua, ENS de Lyon): PR #1308
• KOKKOS package bugfixes and enhancements (Stan Moore, SNL): PR #1277 , PR #1263
• documentation updates (various): PR #1282, PR #1299, PR #1274
• rename pair style lebedeva/z sources to be consistent with style name: PR #1276
• optimization/enhancement for compute entropy/atom for certain settings (Pablo Piaggi, EPFL): PR #1309
• optimization of the create_atoms command for small regions in large boxes (Axel Kohlmeyer, ICTP): PR #1279
• support memory->grow() for 4d-arrays (Adrian Diaz, U Florida): PR #1285
• refactoring of Install.py scripts in lib folders to use the python argparse module and replace calls to subshells with packages, os, shutil, tarfile and others. This makes those scripts independent of local tools. (Axel Kohlmeyer, Temple U): PR #1290
• documentation updates, many small bugfixes (Axel Kohlmeyer, Temple U): PR #1282

Backward compatibility notices:

• moltemplate is no longer bundled with LAMMPS
• the meaning of arguments for Install.py in lib/kim is slightly changed for complex usage cases

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