When reading this file, a different format is expected: lammps_dump = read(filepath_net, format="lammps-dump-text", index=":")
If the read format were to be changed to xyz, matching the implied file type, load_with_cell throws errors as the .xyz and .pdb files written do not contain the required lattice information.
The custom LAMMPS dump style contains the required lattice information, as well as matching the lammps-dump-text format expected. By default, this is typically already used to create files such as nve_t290_vel_dump.lammpstrj at the same time as nve_t290_xyz_dump.lammpstrj, so this can instead be used for filepath_net.
The current example in https://github.com/stfc/CC_HDNNP/blob/main/examples/example_directory/scripts/workflow.ipynb uses:
filepath_net = f"../{lammps_sub_directory}/nve_t290_xyz_dump.lammpstrj", but this appears to refer to a .xyz file. This has two problems:lammps_dump = read(filepath_net, format="lammps-dump-text", index=":")xyz, matching the implied file type,load_with_cellthrows errors as the .xyz and .pdb files written do not contain the required lattice information.The
customLAMMPS dump style contains the required lattice information, as well as matching thelammps-dump-textformat expected. By default, this is typically already used to create files such asnve_t290_vel_dump.lammpstrjat the same time asnve_t290_xyz_dump.lammpstrj, so this can instead be used forfilepath_net.