Dear All,
I have a system in which one bead is connected to other beads using 30 to 50 harmonic bonds. When LAMMPS (17 Feb 2022) reads my data file, I see the below message on my log file, what does max bonds/atom mean? do we have a limitation on LAMMPS for the maximum bonds that each atom can have?
scanning bonds …
30 = max bonds/atom
scanning angles …
10 = max angles/atom
In LAMMPS topology information (bonds/angles/dihedrals/impropers/exclusions) is stored with individual atoms so it can migrate between subdomains and no global communication is needed that would limit parallel scaling to larger numbers of MPI processes. This can be either one atom per item, or all affected atoms (this depends on the settings for the “newton” command). How many bonds are stored with an atom is a property that is determined dynamically before the simulation box is created and then locked in (hence the options to reserve extra storage for additional items with the “create_box” or “read_data” commands). For “read_data” this has the consequence that the data file is read twice: first to determine the settings needed and then a second time to actually read and store the data. The first read creates the output for informational purposes.
Yes and no. The is no general limit, but once the value is set and the simulation box created, it cannot be increased. That might be needed when reading two data files or using molecule templates with more bonds per atom as available based on the locked in setting.