kim init {modelname} metal unit_conversion_mode

boundary p p p

box tilt large

neigh_modify one 4000

variable box_xlo equal {box_xlo}
variable box_xhi equal {box_xhi}
variable box_ylo equal {box_ylo}
variable box_yhi equal {box_yhi}
variable box_zlo equal {box_zlo}
variable box_zhi equal {box_zhi}
variable  box_xy equal  {box_xy}
variable  box_xz equal  {box_xz}
variable  box_yz equal  {box_yz}

region box prism ${{box_xlo}} ${{box_xhi}} &
                 ${{box_ylo}} ${{box_yhi}} &
                 ${{box_zlo}} ${{box_zhi}} &
                 ${{box_xy}} ${{box_xz}} ${{box_yz}}

create_box {numelements} box

read_dump {lammps_xyzfile} 0 x y z box no add yes format xyz

group all region box

{set_masses}

variable xyfinal equal xy*${{_u_distance}}
variable xzfinal equal xz*${{_u_distance}}
variable yzfinal equal yz*${{_u_distance}}

change_box all x scale ${{_u_distance}} &
               y scale ${{_u_distance}} &
               z scale ${{_u_distance}} &
               xy final ${{xyfinal}} &
               xz final ${{xzfinal}} &
               yz final ${{yzfinal}} &
               remap

atom_modify sort 0 0

kim interactions {symbol}

# 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
# thermo output and 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 {dumpfile} 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

run 0