LAMMPS (18 Jun 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task clear OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task # 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_pressure equal 1.0 dimension 3 boundary p p p # 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 # Adjust input variables for possible units changes with Simulator Models variable lattice_constant_converted equal 4.0469995588064185*${_u_distance} variable lattice_constant_converted equal 4.0469995588064185*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 39.85832317861599*${_u_distance} variable xmax_converted equal 39.85832317861599*1 variable ymin_converted equal -79.72069335679079*${_u_distance} variable ymin_converted equal -79.72069335679079*1 variable ymax_converted equal 79.72069335679079*${_u_distance} variable ymax_converted equal 79.72069335679079*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.0469995588064185*${_u_distance} variable zmax_converted equal 4.0469995588064185*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04699955880642 Lattice spacing in x,y,z = 4.047 4.047 4.047 region whole block ${xmin_converted} ${xmax_converted} ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 ${xmax_converted} ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 39.858323178616 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 39.858323178616 -79.7206933567908 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 39.858323178616 -79.7206933567908 79.7206933567908 ${zmin_converted} ${zmax_converted} units box region whole block 0 39.858323178616 -79.7206933567908 79.7206933567908 0 ${zmax_converted} units box region whole block 0 39.858323178616 -79.7206933567908 79.7206933567908 0 4.04699955880642 units box create_box 2 whole Created orthogonal box = (0 -79.7207 0) to (39.8583 79.7207 4.047) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 ${ymax_converted} INF INF units box region upper block INF INF 0.0 79.7206933567908 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 -4 0 orient y 4 9 0 orient z 0 0 1 lattice fcc 4.04699955880642 orient x 9 -4 0 orient y 4 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.34184 5.34184 4.047 create_atoms 1 region upper Created 778 atoms create_atoms CPU = 0.000254154 secs group upper type 1 778 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 4.431986010808247 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -79.7206933567908 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 4 0 orient y -4 9 0 orient z 0 0 1 lattice fcc 4.04699955880642 orient x 9 4 0 orient y -4 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.34184 5.34184 4.047 create_atoms 2 region lower Created 778 atoms create_atoms CPU = 0.000149012 secs group lower type 2 778 atoms in group lower displace_atoms lower move -4.431986010808247 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style meam/c pair_coeff * * ./SM_871795249052_000-files/b'library.NAlTi' N Al Ti ./SM_871795249052_000-files/b'meam.NAlTi' Al Al variable neigh_skin_converted equal 2.0*${_u_distance} variable neigh_skin_converted equal 2.0*1 neighbor ${neigh_skin_converted} bin neighbor 2 bin neigh_modify delay 10 check yes variable delete_distance equal 0.5*${lattice_constant_converted} variable delete_distance equal 0.5*4.04699955880642 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02349977940321 all all Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 12 45 2 3 neighbor lists, perpetual/occasional/extra = 2 1 0 (1) command delete_atoms, occasional, copy from (2) attributes: full, newton on pair build: copy stencil: none bin: none (2) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) pair meam/c, perpetual, half/full from (2) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Deleted 14 atoms, new total = 1542 min_style cg minimize 1e-15 1e-15 5000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 12 45 2 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/c, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 13.7 | 13.7 | 13.7 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5142.0401 0 -5142.0401 2678.5317 378 0 -5168.2016 0 -5168.2016 -2026.137 Loop time of 18.5636 on 1 procs for 378 steps with 1542 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5142.04012001 -5168.20159046 -5168.20159046 Force two-norm initial, final = 30.8992 8.28521e-06 Force max component initial, final = 6.27938 1.78831e-06 Final line search alpha, max atom move = 1 1.78831e-06 Iterations, force evaluations = 378 747 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.497 | 18.497 | 18.497 | 0.0 | 99.64 Neigh | 0.0032148 | 0.0032148 | 0.0032148 | 0.0 | 0.02 Comm | 0.03791 | 0.03791 | 0.03791 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02552 | | | 0.14 Nlocal: 1542 ave 1542 max 1542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8683 ave 8683 max 8683 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 65916 ave 65916 max 65916 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 131832 ave 131832 max 131832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 131832 Ave neighs/atom = 85.4942 Neighbor list builds = 1 Dangerous builds = 0 fix 1 all box/relax x 0.0 z 0.0 couple none vmax 0.001 minimize 1.0e-25 1.0e-25 1000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Per MPI rank memory allocation (min/avg/max) = 13.7 | 13.7 | 13.7 Mbytes Step Temp E_pair E_mol TotEng Press Volume 378 0 -5168.2016 0 -5168.2016 -2026.137 25718.951 1378 0 -5168.2506 0 -5168.2506 21.338262 25651.311 Loop time of 50.778 on 1 procs for 1000 steps with 1542 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -5168.20159046 -5168.2506124 -5168.2506124 Force two-norm initial, final = 52.1402 0.00352773 Force max component initial, final = 38.9988 0.0021765 Final line search alpha, max atom move = 0.254799 0.000554569 Iterations, force evaluations = 1000 1999 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 50.339 | 50.339 | 50.339 | 0.0 | 99.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.097338 | 0.097338 | 0.097338 | 0.0 | 0.19 Output | 1.9789e-05 | 1.9789e-05 | 1.9789e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3412 | | | 0.67 Nlocal: 1542 ave 1542 max 1542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9061 ave 9061 max 9061 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 65996 ave 65996 max 65996 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 131992 ave 131992 max 131992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 131992 Ave neighs/atom = 85.5979 Neighbor list builds = 0 Dangerous builds = 0 unfix 1 # Variables used to rescale the positions and energies so that the quantities # in the dumpfile are in the original metal units (angstrom and eV) # even if we're running with a Simulator Model that uses different units variable pe_metal equal "c_thermo_pe/v__u_energy" variable lx_metal equal lx/${_u_distance} variable lx_metal equal lx/1 variable ly_metal equal ly/${_u_distance} variable ly_metal equal ly/1 variable lz_metal equal lz/${_u_distance} variable lz_metal equal lz/1 variable press_metal equal "c_thermo_press/v__u_pressure" variable pxx_metal equal pxx/${_u_pressure} variable pxx_metal equal pxx/1 variable pyy_metal equal pyy/${_u_pressure} variable pyy_metal equal pyy/1 variable pzz_metal equal pzz/${_u_pressure} variable pzz_metal equal pzz/1 variable mass_metal atom mass/${_u_mass} variable mass_metal atom mass/1 compute csym all centro/atom fcc compute particle_eng all pe/atom compute particle_engsum all reduce sum c_particle_eng compute csymsum all reduce sum c_csym compute distance all pair/local dist compute mindist all reduce min c_distance # Isolated atom energy in eV (no unit conversion necessary) variable isolated_atom_energy equal 0.0 variable particle_eng_metal atom "c_particle_eng/v__u_energy - v_isolated_atom_energy" variable csym_metal atom c_csym/(${_u_distance}*${_u_distance}) variable csym_metal atom c_csym/(1*${_u_distance}) variable csym_metal atom c_csym/(1*1) variable csymsum_metal equal c_csymsum/(${_u_distance}*${_u_distance}) variable csymsum_metal equal c_csymsum/(1*${_u_distance}) variable csymsum_metal equal c_csymsum/(1*1) variable mindist_metal equal c_mindist/${_u_distance} variable mindist_metal equal c_mindist/1 reset_timestep 0 run 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 12 45 2 4 neighbor lists, perpetual/occasional/extra = 2 2 0 (1) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/c, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none (3) compute centro/atom, occasional, copy from (1) attributes: full, newton on pair build: copy stencil: none bin: none (4) compute pair/local, occasional, copy from (2) attributes: half, newton on pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 12.58 | 12.58 | 12.58 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5168.2506 0 -5168.2506 21.338262 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1542 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.146e-06 | | |100.00 Nlocal: 1542 ave 1542 max 1542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9306 ave 9306 max 9306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 66006 ave 66006 max 66006 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 132012 ave 132012 max 132012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 132012 Ave neighs/atom = 85.6109 Neighbor list builds = 0 Dangerous builds = 0 thermo 0 thermo_style custom step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal run 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Per MPI rank memory allocation (min/avg/max) = 12.58 | 12.58 | 12.58 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -5168.2506 -5168.2506 39.814941 159.44139 4.0407541 21.338262 21.338262 0.039863633 63.839189 0.13573378 2.4189873 674.93818 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1542 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Nlocal: 1542 ave 1542 max 1542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9306 ave 9306 max 9306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 66006 ave 66006 max 66006 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 132012 ave 132012 max 132012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 132012 Ave neighs/atom = 85.6109 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_047.9250/numatoms.out 1542 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5168.25061240441-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5168.25061240441-1542*${isolated_atom_energy} variable adjusted_pe_metal equal -5168.25061240441-1542*0 print "${adjusted_pe_metal} eV" file output/dump_047.9250/energy.out -5168.25061240441 eV print "${mindist_metal} Angstroms" file output/dump_047.9250/mindistance.out 2.41898734957281 Angstroms write_dump all cfg output/dump_047.9250/dump_post.cfg mass type xs ys zs id v_mass_metal v_csym_metal v_particle_eng_metal modify element Al Al print "This indicates that LAMMPS ran successfully" file output/dump_047.9250/success.out This indicates that LAMMPS ran successfully Total wall time: 0:01:09