# The units we assume we'll use. The kim-lammps-preprocessor may swap this line out if # running against a Simulator Model whose units are not 'metal' units metal # Variables that can be adjusted by kim-lammps-preprocessor to switch unit sets for # Simulator Models variable _u_distance equal 1.0 variable _u_energy equal 1.0 variable _u_mass equal 1.0 variable _u_force equal 1.0 # This line may be swapped out by kim-lammps-preprocessor if running against a Simulator # Model whose atom_style is not 'atomic' atom_style atomic boundary p p p box tilt large neigh_modify one 4000 variable box_xlo equal 0.0 variable box_xhi equal 5.47042 variable box_ylo equal 0.0 variable box_yhi equal 5.3888 variable box_zlo equal 0.0 variable box_zhi equal 5.39218 variable box_xy equal 0.0146058 variable box_xz equal 0.134413 variable box_yz equal -0.103851 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 ${yzfinal} & remap atom_modify sort 0 0 pair_style kim Sim_LAMMPS_ADP_StarikovLopanitsynaSmirnova_2018_SiAu__SM_985135773293_000 pair_coeff * * Si # Use nsq neighlist method instead of binning since this is a small system variable neigh_skin equal 2.0*${_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