kim init SW_ZhangXieHu_2014OptimizedSW1_Si__MO_800412945727_005 metal unit_conversion_mode boundary p p p box tilt large neigh_modify one 4000 variable box_xlo equal 0.0 variable box_xhi equal 3.0839 variable box_ylo equal 0.0 variable box_yhi equal 3.17138 variable box_zlo equal 0.0 variable box_zhi equal 3.06669 variable box_xy equal 0.0102376 variable box_xz equal 0.127489 variable box_yz equal 0.0401208 region box prism \${box_xlo} \${box_xhi} & \${box_ylo} \${box_yhi} & \${box_zlo} \${box_zhi} & \${box_xy} \${box_xz} \${box_yz} create_box 1 box read_dump output/lammps_inputs/triclinicpbc_lammps.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} 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 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 # 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 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 run 0