kim init Tersoff_LAMMPS_ErhartAlbe_2005SiII_SiC__MO_408791041969_004 metal unit_conversion_mode boundary f f f variable boxextent equal 25.0 region box block -\${boxextent} \${boxextent} & -\${boxextent} \${boxextent} & -\${boxextent} \${boxextent} create_box 1 box read_dump output/lammps_inputs/cluster.xyz 0 x y z box no add yes format xyz group all region box variable mass1_converted equal 28.0855*\${_u_mass} mass 1 \${mass1_converted} change_box all x scale \${_u_distance} & y scale \${_u_distance} & z scale \${_u_distance} & remap atom_modify sort 0 0 kim interactions Si # Use nsq neighlist method instead of binning since this is a small system variable neigh_skin equal 2.0*\${_u_distance} neighbor \${neigh_skin} nsq # Variables used to rescale the positions and forces so that the quantities in the # dumpfile are in the original metal units (angstrom and eV/angstrom) even if we're # running with a Simulator Model that uses different units variable pe_metal equal "c_thermo_pe/v__u_energy" variable x_metal atom x/\${_u_distance} variable y_metal atom y/\${_u_distance} variable z_metal atom z/\${_u_distance} variable fx_metal atom fx/\${_u_force} variable fy_metal atom fy/\${_u_force} variable fz_metal atom fz/\${_u_force} dump dumpid all custom 1 output/lammps_dump/lammps.dump id type v_x_metal v_y_metal v_z_metal & v_fx_metal v_fy_metal v_fz_metal dump_modify dumpid sort id format line "%d %d %16.7f %16.7f %16.7f %16.7f %16.7f %16.7f" thermo_style custom v_pe_metal # Define minimization (note that etol is actually unitless, but ftol has units of force) min_style cg variable dmax equal 0.1*\${_u_distance} min_modify dmax \${dmax} variable ftol equal 1e-10*\${_u_force} minimize 1e-10 \${ftol} 2000 100000