LAMMPS Files

This is the fourth update to the 29 August 2024 stable release that fixes more bugs that have been reported since then and updates some libraries, dependencies, tools, and build system support.

The following individual changes are included:

• fix issue in fix bond/react to require per-atom masses in molecule file when the system uses per-atom masses
• error out in compute msd if the number of atoms in the compute group changes by other means than a dynamic group
• avoid crash in utils::split_words() when processing partially quoted text
• fix bug in fix halt that would reset the timer timeout, even if it didn't trigger it
• fix bug in Fortran module where reallocation of global fix callback list did not happen as expected
• make pair styles (like EAM, MEAM, BOP, etc.) that call atom->set_mass() compatible with per-atom masses
• fix issue of yaml-cpp library included in ML-PACE failing to compile with GCC 15+
• bugfixes and LAMMPS-GUI optimizations and refactoring imported from upstream. It is now at version 1.7.0
• fix out-of-bounds access in initializing the cvatom array in pair.cpp, angle.cpp, dihedral.cpp, and improper.cpp
• updates of molecule command backported from upstream:
• honor atom-id when parsing sections consistently
• make parsing of header keywords more specific and thus don't misread incorrect ones
• error out when the required "atoms" header keyword is missing
• Masses section is required for body particles
• update the count of bodies when using create_atoms, fix deposit, or fix pour with a molecule template for body particles
• make python unit tests compatible with mpi4py version 4
• various fixes to classes where virtual and override were missing or used incorrectly as flagged by static code analysis
• various incorrect types or use of utils::numeric() instead of utils::inumeric() as flagged by static code analysis
• recognize a couple more Windows build numbers
• add caching for tpcpu and spcpu thermo keywords, so they can be used multiple times